[med-svn] r22740 - in trunk/packages/rostlab/profphd/trunk/debian: . patches tests

Tatiana Malygina latticetower-guest at moszumanska.debian.org
Thu Sep 1 20:03:53 UTC 2016 

Author: latticetower-guest
Date: 2016-09-01 20:03:52 +0000 (Thu, 01 Sep 2016)
New Revision: 22740

Added:
   trunk/packages/rostlab/profphd/trunk/debian/patches/5_fix_regex_warning.patch
   trunk/packages/rostlab/profphd/trunk/debian/tests/profphd-install-test
Modified:
   trunk/packages/rostlab/profphd/trunk/debian/changelog
   trunk/packages/rostlab/profphd/trunk/debian/patches/3_fix_indexing.patch
   trunk/packages/rostlab/profphd/trunk/debian/patches/series
   trunk/packages/rostlab/profphd/trunk/debian/tests/control
Log:
fixed patch for usage of perl 5.20-5.22, fix warnings and tests - work in progress

Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/changelog	2016-09-01 15:05:54 UTC (rev 22739)
+++ trunk/packages/rostlab/profphd/trunk/debian/changelog	2016-09-01 20:03:52 UTC (rev 22740)
@@ -6,6 +6,10 @@
   * add hardening in d/rules
   * add patches 1-4 to use latest perl 5.22 (UNFINISHED! checking if this works) 
   * add debian/tests (unfinished too)
+  * fix in patches/3_fix_indexing.patch (I think I managed to reproduce the 
+    reason of error), add patch 5_fix_regex_warning.patch,
+    move working portion of tests from test-install.pl script to 
+    tests/profphd-install-test
 
  -- Tatiana Malygina <merlettaia at gmail.com>  Fri, 08 Jul 2016 22:46:36 +0300
 

Modified: trunk/packages/rostlab/profphd/trunk/debian/patches/3_fix_indexing.patch
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/patches/3_fix_indexing.patch	2016-09-01 15:05:54 UTC (rev 22739)
+++ trunk/packages/rostlab/profphd/trunk/debian/patches/3_fix_indexing.patch	2016-09-01 20:03:52 UTC (rev 22740)
@@ -1,27 +1,45 @@
 Author: Tatiana Malygina <merlettaia at gmail.com>
 Description: fix error "Modification of non-creatable array value attempted, 
  subscript -1 at /usr/share/profphd/prof/scr/lib/lib-prof.pl line 7739"
-Last-Update: 2016-08-23
+Last-Update: 2016-08-29
 
---- a/src/prof/scr/lib/lib-prof.pl
-+++ b/src/prof/scr/lib/lib-prof.pl
-@@ -7736,7 +7737,7 @@
+--- profphd-1.0.42.orig/src/prof/scr/lib/lib-prof.pl
++++ profphd-1.0.42/src/prof/scr/lib/lib-prof.pl
+@@ -7720,7 +7720,7 @@
+ 
+ 				# --------------------------------------------------
+ 				# get helix lengths
+-    $#tmpbeg=$#tmpbeg=$#tmpend=$prev=$cth=0;
++    $#tmpbeg=$prev=$cth=0; $#tmpend=$#tmplen=1;
+     foreach $itres (1..$rdb{"NROWS"}){
+ 	next if ($prof_skip{$itres} || ! defined $rdb{$itres,"PHEL"});
+ 	if    ($rdb{$itres,"PHEL"} ne "H") {
+@@ -7736,7 +7736,7 @@
  	    ++$tmplen[$cth];}
      }
  				# set last
 -    $tmpend[$cth]=$tmplen[$cth] if (! defined $tmpend[$cth]);
-+    $tmpend[$cth]=$tmplen[$cth] if (! defined $tmpend[$cth] && $cth >= $[ );
++    $tmpend[$cth]=$tmplen[$cth] if (! defined $tmpend[$cth] );
  				# --------------------------------------------------
  				# find short ones
      foreach $it (1..$#tmpbeg){
-@@ -7847,8 +7848,8 @@
+@@ -7832,7 +7832,7 @@
+ 
+ 				# --------------------------------------------------
+ 				# get helix lengths
+-    $#tmpbeg=$#tmpbeg=$#tmpend=$prev=$cte=0;
++    $#tmpbeg=$prev=$cte=0; $#tmpend=$#tmplen=1;
+     foreach $itres (1..$rdb{"NROWS"}){
+ 	next if ($prof_skip{$itres} || ! defined $rdb{$itres,"PHEL"});
+ 	if    ($rdb{$itres,"PHEL"} ne "E") {
+@@ -7847,8 +7847,8 @@
  	else {
  	    ++$tmplen[$cte];}
      }
 -				# set last
 -    $tmpend[$cte]=$tmplen[$cte] if (! defined $tmpend[$cte]);
 +		# set last
-+    $tmpend[$cte]=$tmplen[$cte] if (! defined $tmpend[$cte] && $cte >= $[ );
++    $tmpend[$cte]=$tmplen[$cte] if (! defined $tmpend[$cte] );
  				# --------------------------------------------------
  				# find short ones
      foreach $it (1..$#tmpbeg){

Added: trunk/packages/rostlab/profphd/trunk/debian/patches/5_fix_regex_warning.patch
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/patches/5_fix_regex_warning.patch	                        (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/patches/5_fix_regex_warning.patch	2016-09-01 20:03:52 UTC (rev 22740)
@@ -0,0 +1,11 @@
+--- profphd-1.0.42.orig/src/prof/scr/lib/lib-profwrt.pl
++++ profphd-1.0.42/src/prof/scr/lib/lib-profwrt.pl
+@@ -2300,7 +2300,7 @@
+ 				# long lines: to split
+ 	    $lentmp=$len-12;
+ 	    while (length($tmp)>=$len){
+-		$tmp=~s/^(.{$lentmp}?\S*[\., \-\;\:])//;
++		$tmp=~s/^(.{$lentmp}\S*[\., \-\;\:])//;
+ 		last if (! defined $1);
+ 		print $fhoutLoc 
+ 		    $1. " " x ($len-length($1))  ."#\n";

Modified: trunk/packages/rostlab/profphd/trunk/debian/patches/series
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/patches/series	2016-09-01 15:05:54 UTC (rev 22739)
+++ trunk/packages/rostlab/profphd/trunk/debian/patches/series	2016-09-01 20:03:52 UTC (rev 22740)
@@ -2,3 +2,4 @@
 2_remove_perlbrew_usage.patch
 3_fix_indexing.patch
 4_fix_negative_repeat_count.patch
+5_fix_regex_warning.patch

Modified: trunk/packages/rostlab/profphd/trunk/debian/tests/control
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/tests/control	2016-09-01 15:05:54 UTC (rev 22739)
+++ trunk/packages/rostlab/profphd/trunk/debian/tests/control	2016-09-01 20:03:52 UTC (rev 22740)
@@ -1,9 +1,6 @@
-Tests: installation-test
+Tests: installation-test, profphd-install-test
 Depends: @, pp-popularity-contest
 
-Test-Command: perl /usr/share/profphd/prof/scr/test-install.pl do
-Depends: @, pp-popularity-contest
-
 Test-Command: /usr/share/pkg-perl-autopkgtest/runner build-deps
 Depends: @, @builddeps@, pkg-perl-autopkgtest, pp-popularity-contest
 

Added: trunk/packages/rostlab/profphd/trunk/debian/tests/profphd-install-test
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/tests/profphd-install-test	                        (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/tests/profphd-install-test	2016-09-01 20:03:52 UTC (rev 22740)
@@ -0,0 +1,55 @@
+#!/bin/sh
+# autopkgtest check: build and run with default test data
+# This test is similar to installation test, yet it differs: it loads tests commands
+# from current version of test-install.pl and checks the results.
+# Author: Tatiana Malygina <merlettaia at gmail.com>
+
+set -e
+
+pkg=profphd
+
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cd $ADTTMP
+
+cp -a /usr/share/${pkg}/prof/exa/* .
+find . -type f -name "*.gz" -exec gunzip \{\} \;
+for lnk in `find . -type l -name "*.gz"` ; do
+    ln -s `basename $(readlink $lnk) .gz` `echo $lnk | sed 's/\.gz$//'`
+    rm $lnk
+done
+
+
+prof 1ppt.hssp fileRdb=tst-1ppt.rdbProfSec sec ascii
+[ -z $(cmp -s tst-1ppt.rdbProfSec 1ppt.hssp.prof) ]
+#Useless use of greediness modifier '?' in regex; marked by <-- HERE in m/^(.{59}? <-- HERE \S*[\., \-\;\:])/ at /usr/share/profphd/prof/scr/lib/lib-profwrt.pl line 2303.
+prof 1ppt.hssp fileRdb=tst-1ppt.rdbProfAcc acc ascii
+[ -s tst-1ppt.rdbProfAcc ]
+#Useless use of greediness modifier '?' in regex; marked by <-- HERE in m/^(.{59}? <-- HERE \S*[\., \-\;\:])/ at /usr/share/profphd/prof/scr/lib/lib-profwrt.pl line 2303.
+prof 1ppt.hssp fileRdb=tst-1ppt.rdbProfBoth both ascii
+[ -s tst-1ppt.rdbProfBoth ]
+#Useless use of greediness modifier '?' in regex; marked by <-- HERE in m/^(.{59}? <-- HERE \S*[\., \-\;\:])/ at /usr/share/profphd/prof/scr/lib/lib-profwrt.pl line 2303.
+prof 1ppt.hssp fileRdb=tst-1ppt.rdbProf ascii
+[ -s tst-1ppt.rdbProf ]
+#Useless use of greediness modifier '?' in regex; marked by <-- HERE in m/^(.{59}? <-- HERE \S*[\., \-\;\:])/ at /usr/share/profphd/prof/scr/lib/lib-profwrt.pl line 2303.
+#prof 1prc.hssp_L fileRdb=tst-1prcL.rdbProfSec sec ascii
+#prof 1prc.hssp_L fileRdb=tst-1prcL.rdbProfAcc acc ascii
+#prof 1prc.hssp_L fileRdb=tst-1prcL.rdbProfHtm htm ascii
+#prof 1prc.hssp_L fileRdb=tst-1prcL.rdbProf ascii
+#prof 1shg.hssp fileRdb=tst-1shg.rdbProf both ascii saf fileAli=tst-1shg.profSaf dssp fileDssp=tst-1shg.profDssp
+#prof 1shg.hssp fileRdb=tst-1shg.rdbProfFilter both ascii filter optFilter=red=70 msf fileAli=tst-1shg.profFilterMsf
+#prof 256b.dssp fileRdb=tst-256b.rdbProfSec sec ascii
+echo "next examples"
+#Useless use of greediness modifier '?' in regex; marked by <-- HERE in m/^(.{59}? <-- HERE \S*[\., \-\;\:])/ at /usr/share/profphd/prof/scr/lib/lib-profwrt.pl line 2303.
+prof 2ppt.fastamul fileRdb=tst-2ppt.rdbProfSec sec ascii
+[ -z $(cmp -s tst-2ppt.rdbProfSec 2ppt.rdbProfSec) ]
+#Useless use of greediness modifier '?' in regex; marked by <-- HERE in m/^(.{59}? <-- HERE \S*[\., \-\;\:])/ at /usr/share/profphd/prof/scr/lib/lib-profwrt.pl line 2303.
+prof 8rnt.msf fileRdb=tst-8rnt.rdbProfSec sec ascii
+#Redundant argument in printf at /usr/share/perl5/RG/Utils/Copf.pm line 6536.
+#Redundant argument in printf at /usr/share/perl5/RG/Utils/Copf.pm line 6308.
+#Useless use of greediness modifier '?' in regex; marked by <-- HERE in m/^(.{59}? <-- HERE \S*[\., \-\;\:])/ at /usr/share/profphd/prof/scr/lib/lib-profwrt.pl line 2303.
+prof 9rnt.saf fileRdb=tst-9rnt.rdbProfSec sec ascii
+# Useless use of greediness modifier '?' in regex; marked by <-- HERE in m/^(.{59}? <-- HERE \S*[\., \-\;\:])/ at /usr/share/profphd/prof/scr/lib/lib-profwrt.pl line 2303.

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